/* @func embPatternSeqCompile *************************************************
**
** Adds compiled pattern into AjPPattern.
**
** @param [w] pat [AjPPatternSeq] Pattern for compiling
** @return [AjBool] True, if compilation succeeded
** @@
******************************************************************************/
AjBool embPatternSeqCompile (AjPPatternSeq pat)
{
AjPPatComp embpat;
AjBool embType;
AjPStr pattern = NULL;
ajStrAssignS(&pattern,ajPatternSeqGetPattern(pat));
ajStrFmtUpper(&pattern);
ajDebug("embPatlistSeqCompile: name %S, pattern %S\n",
ajPatternSeqGetName(pat),pattern);
embpat = ajPatCompNew();
if (ajPatternSeqGetProtein(pat))
embType=ajTrue;
else
embType=ajFalse;
if (!embPatGetTypeII(embpat,pattern,
ajPatternSeqGetMismatch(pat),embType))
{
ajDebug("embPatlistSeqCompile: Illegal pattern %S: '%S'\n",
ajPatternSeqGetName(pat),ajPatternSeqGetPattern(pat));
ajPatCompDel(&embpat);
ajStrDel(&pattern);
return ajFalse;
}
embPatCompileII(embpat,ajPatternSeqGetMismatch(pat));
ajPatternSeqSetCompiled(pat,embpat);
ajStrDel(&pattern);
return ajTrue;
}
ajuint ajPatlistSeqDoc (AjPPatlistSeq plist, AjPStr* Pdoc)
{
AjPPatternSeq pat = NULL;
ajFmtPrintS(Pdoc, "%-12s %8s %s\n",
"Pattern_name", "Mismatch", "Pattern");
while (ajPatlistSeqGetNext(plist, &pat))
{
ajFmtPrintAppS(Pdoc, "%-12S %8d %S\n",
ajPatternSeqGetName(pat),
ajPatternSeqGetMismatch(pat),
ajPatternSeqGetPattern(pat));
}
return ajListGetLength(plist->Patlist);
}
void embPatternSeqSearch (AjPFeattable ftable, const AjPSeq seq,
const AjPPatternSeq pat, AjBool reverse)
{
const void *tidy;
ajuint hits;
ajuint i;
AjPPatComp pattern;
EmbPMatMatch m = NULL;
AjPFeature sf = NULL;
AjPSeq revseq = NULL;
AjPList list = ajListNew();
AjPStr seqstr = ajStrNew();
AjPStr seqname = ajStrNew();
AjPStr tmp = ajStrNew();
ajint adj;
ajint begin;
AjBool isreversed;
ajint seqlen;
seqlen = ajSeqGetLen(seq);
if(!seqlen)
return;
isreversed = ajSeqIsReversedTrue(seq);
if(isreversed)
seqlen += ajSeqGetOffset(seq);
begin = ajSeqGetBeginTrue(seq);
adj = ajSeqGetEndTrue(seq);
if(!ajStrGetLen(featMotifProt))
ajStrAssignC(&featMotifProt, "SO:0001067");
if(!ajStrGetLen(featMotifNuc))
ajStrAssignC(&featMotifNuc, "SO:0000714");
ajStrAssignS(&seqname,ajSeqGetNameS(seq));
pattern = ajPatternSeqGetCompiled(pat);
if (reverse)
{
revseq = ajSeqNewSeq(seq);
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(revseq),
begin-1,adj-1);
ajSeqstrReverse(&seqstr);
}
else
ajStrAssignSubS(&seqstr, ajSeqGetSeqS(seq),
begin-1,adj-1);
ajStrFmtUpper(&seqstr);
/*ajDebug("seqlen:%d len: %d offset: %d offend: %d begin: %d end: %d\n"
"'%S'\n",
seqlen , ajSeqGetLen(seq), ajSeqGetOffset(seq),
ajSeqGetOffend(seq), ajSeqGetBegin(seq), ajSeqGetEnd(seq),
seqstr);*/
ajDebug("embPatternSeqSearch '%S' protein: %B reverse: %B\n",
pattern->pattern, pat->Protein, reverse);
embPatFuzzSearchII(pattern,begin,seqname,seqstr,list,
ajPatternSeqGetMismatch(pat),&hits,&tidy);
ajDebug ("embPatternSeqSearch: found %d hits\n",hits);
if(!reverse)
ajListReverse(list);
for(i=0;i<hits;++i)
{
ajListPop(list,(void **)&m);
if (reverse)
sf = ajFeatNew(ftable, NULL, featMotifNuc,
adj - m->start - m->len + begin + 1,
adj - m->start + begin,
0.0, '-', 0);
else
{
if(ajSeqIsProt(seq) || ajFeattableIsProt(ftable))
sf = ajFeatNewProt(ftable, NULL, featMotifProt,
m->start,
m->start + m->len - 1,
0.0);
else
sf = ajFeatNew(ftable, NULL, featMotifNuc,
m->start,
m->start + m->len - 1,
0.0, '.', 0);
}
if(isreversed)
ajFeatReverse(sf, seqlen);
/*
ajUser("isrev: %B reverse: %B begin: %d adj: %d "
"start: %d len: %d seqlen: %d %d..%d '%c'\n",
isreversed, reverse, begin, adj, m->start, m->len, seqlen,
sf->Start, sf->End, sf->Strand);
*/
ajFeatSetScore(sf, (float) (m->len - m->mm));
ajFmtPrintS(&tmp, "*pat %S: %S",
ajPatternSeqGetName(pat),
ajPatternSeqGetPattern(pat));
ajFeatTagAdd(sf,NULL,tmp);
if(m->mm)
{
ajFmtPrintS(&tmp, "*mismatch %d", m->mm);
ajFeatTagAdd(sf, NULL, tmp);
}
embMatMatchDel(&m);
}
ajStrDel(&seqname);
ajStrDel(&seqstr);
ajStrDel(&tmp);
ajListFree(&list);
if (reverse)
ajSeqDel(&revseq);
return;
}
